Megumi Yokota’s mother with pictures of the girl who was abducted when she was 13. North Korea claimed she killed herself in 1994 but tests on her alleged remains showed they contained someone else’s DNA.
Photograph: Katsumi Kasahara/AP

A Japanese newspaper claims it has uncovered evidence that North Korea systematically abducted foreign citizens under its former leader, Kim Jong-il.

The Tokyo Shimbun said it had acquired a secret manual, thought to have been written in the late 1990s, that instructs spies how to carry out abductions on foreign soil and evade capture.

The newspaper’s report, published this week, lends weight to claims by Japan that the regime had a well-organised network of spies trained to seize foreigners, including dozens of Japanese, and that the abductions were not the work of rogue agents.

Japan suspects that 17 of its citizens were snatched in the 1970s and 80s, and taken to North Korea to teach their language and customs to help agents blend in while on assignment in Japan.

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The 356-page classified document was used at the Kim Jong-il Political-Military University, a secretive North Korean intelligence institute, the newspaper reported.

According to NK News, one section coaches spies on how to conduct overseas abductions, advising them: “To abduct the target, one has to know the target’s address, where the target enters and exits, day-to-day traffic routes, means of transportation and their timeline as well.”

It goes on to recommend “terminating” targets who resist, adding that agents should not leave “a single trace” of evidence at the scene.

The Tokyo Shimbun says the document is the first physical evidence that overseas abductions were carried out with the full knowledge and blessing of North Korea’s leadership.

Some, however, have questioned the document’s authenticity, pointing out that the Korean word for “abduction” is written in a style used in South, not North, Korea. In response, the newspaper said it believed the manual was written that way to help its operatives assimilate, as South Korea was the prime target for abductions at the time.

“The people involved in the story are in no doubt that the document is genuine,” a Tokyo Shimbun journalist who reports on North Korea said.

The Japanese government is seeking information about at least 12 people it says were abducted by North Korea. In 2002, the then prime minister, Junichiro Koizumi, secured the release of five other abductees, who were later joined by their families, after a summit in Pyongyang with his counterpart Kim Jong-il.

Japan refuses to believe North Korean claims that eight of the remaining 12 have died, some in mysterious accidents, and the other four had never entered the country. The missing abductees include Megumi Yokota, who was 13 when she was snatched on her way home from school in Niigata, on the Japan Sea coast, in 1977.

North Korea claimed that Yokota had killed herself in 1994 while being treated in hospital for depression. But tests on her alleged remains conducted in Japan in 2004 showed they contained someone else’s DNA. Japanese experts also found inconsistencies in her death certificate.

Yokota is thought to have been taken to a spy training facility in Pyongyang soon after she arrived in North Korea. Kyodo News recently quoted a South Korean source as saying that she studied Korean for about three years and then taught Japanese until the mid-1980s. She married a South Korean abductee, with whom she had a daughter.

Talks between the two countries on resolving the remaining abductions broke down after making no progress. Japan says it will not normalise diplomatic ties with Pyongyang until the abductions have been resolved. It is unclear how the manual could help Japanese negotiators at any future talks, however, as it was written at least 15 years ago.

“But the families of the abductees and their supporters can now point to this document as proof that North Korea systematically organised the abductions,” the Tokyo Shimbun reporter said. “That will enable them to put pressure on the Japanese government to do more to settle the matter.”